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Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal

Christian S Jensen1, Charles J Norsigian2, Xin Fang2

  • 1The Regional Department of Clinical Microbiology, Region Zealand, Slagelse, Denmark.

Frontiers in Genetics
|March 21, 2020
PubMed

Insights

We developed the first genome-scale model for Streptococcus oralis SK141, a bacterium found in the human microbiome. This model accurately predicts gene essentiality and metabolic functions, aiding research into oral bacteria and disease.

Area of Science:

  • Microbiology
  • Systems Biology
  • Computational Biology

Background:

  • The mitis group of streptococci (MGS) are commensal bacteria in the human microbiome.
  • Certain MGS can cause severe infections like infective endocarditis.
  • Genome-scale models are powerful tools for studying bacterial metabolism.

Purpose of the Study:

  • To develop the first genome-scale metabolic model for *Streptococcus oralis* SK141.
  • To validate the model's accuracy using experimental data.
  • To provide a tool for exploring MGS metabolism and interspecies interactions.

Main Methods:

  • Construction of a genome-scale model (iCJ415) for *Streptococcus oralis* SK141.
  • Validation using gene essentiality and amino acid auxotrophy data from related species.
  • Phenotypic testing with Biolog Phenotype microarrays for carbon source utilization.

Main Results:

  • The iCJ415 model achieved 71-76% accuracy in predicting gene essentiality.
  • The model demonstrated 85% accuracy in predicting amino acid auxotrophy.
  • iCJ415 showed 82% accuracy in predicting carbon source utilization.

Conclusions:

  • The iCJ415 model is a validated resource for *Streptococcus oralis* SK141.
  • This model can facilitate research into MGS metabolism and pathogenesis.
  • It offers insights into the complex metabolic interactions within the human oral microbiome.
Keywords:
Biolog phenotypic profilingStreptococcus oralisconstraint-based modelinggenome-scale reconstructionmitis group of streptococci

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